After the publication of Fishman et al. (2001), more loci were genotyped. Now, we will build a new map using the entire dataset using the software OneMap (Margarido et al., 2007). OneMap was the first software developed to simultaneously estimate the linkage and linkage phases (integrated genetic map) between markers in outcrossing species (F1). It has two tutorials that teach step by step how to construct a genetic linkage map in inbreeding and outcrossing populations. You can consult the tutorials here (https://github.com/augusto-garcia/onemap).
library("onemap")
library("gridExtra")
data_map = read_mapmaker(file="m_feb06.raw")
## --Read the following data:
## Type of cross: f2
## Number of individuals: 287
## Number of markers: 418
## Missing trait values:
## fl: 11
## fs: 19
## ft: 11
## ll: 20
## nv: 12
## pa: 35
## pal: 11
## pv: 12
## sa: 11
## sl: 11
## ss: 28
## tl: 11
## tp: 12
## tw: 11
## vi: 12
## ww: 11
data_map
## This is an object of class 'onemap'
## Type of cross: f2
## No. individuals: 287
## No. markers: 418
## CHROM information: no
## POS information: no
## Percent genotyped: 89
##
## Segregation types:
## AA : AB : BB --> 213
## Not AA : AA --> 92
## Not BB : BB --> 113
##
## No. traits: 16
## Missing trait values:
## fl: 11
## fs: 19
## ft: 11
## ll: 20
## nv: 12
## pa: 35
## pal: 11
## pv: 12
## sa: 11
## sl: 11
## ss: 28
## tl: 11
## tp: 12
## tw: 11
## vi: 12
## ww: 11
plot(data_map)
plot_by_segreg_type(data_map)
bins = find_bins(data_map, exact = FALSE)
bins
## This is an object of class 'onemap_bin'
## No. individuals: 287
## No. markers in original dataset: 418
## No. of bins found: 416
## Average of markers per bin: 1.004808
## Type of search performed: non exact
data_bins = create_data_bins(data_map, bins)
data_bins
## This is an object of class 'onemap'
## Type of cross: f2
## No. individuals: 287
## No. markers: 416
## CHROM information: no
## POS information: no
## Percent genotyped: 89
##
## Segregation types:
## AA : AB : BB --> 212
## Not AA : AA --> 92
## Not BB : BB --> 112
##
## No. traits: 16
## Missing trait values:
## fl: 11
## fs: 19
## ft: 11
## ll: 20
## nv: 12
## pa: 35
## pal: 11
## pv: 12
## sa: 11
## sl: 11
## ss: 28
## tl: 11
## tp: 12
## tw: 11
## vi: 12
## ww: 11
data_seg = test_segregation(data_bins)
a = print(data_seg)
head(a, 10)
## Marker H0 Chi-square p-value % genot.
## 1 AA461 3:1 9.6012121 0.0019444897 95.82
## 2 AA420 3:1 0.8836364 0.3472076393 95.82
## 3 AA404 3:1 1.8436364 0.1745253406 95.82
## 4 AA384 3:1 3.9381818 0.0472017677 95.82
## 5 AA378 3:1 12.3648485 0.0004374931 95.82
## 6 AA371C 1:2:1 5.3927273 0.0674503413 95.82
## 7 AA361 3:1 4.8109091 0.0282801226 95.82
## 8 AA341 3:1 2.2412121 0.1343756065 95.82
## 9 AA311 3:1 5.4412121 0.0196670167 95.82
## 10 AA280 3:1 3.4048485 0.0650050838 95.82
Bonferroni_alpha(data_seg)
## [1] 0.0001201923
select_segreg(data_seg, distorted = FALSE)
## [1] "AA461" "AA420" "AA404" "AA384" "AA378" "AA371C"
## [7] "AA361" "AA341" "AA311" "AA280" "AA277" "AA270"
## [13] "AA268" "AA246" "AA208" "AA167" "AA166C" "AA163"
## [19] "AA158" "AA137" "AA100" "AA95" "AA66" "BA497"
## [25] "BA449" "BA445" "BA416" "BA400" "BA394" "BA384"
## [31] "BA374" "BA372" "BA334" "BA314" "BA311" "BA301"
## [37] "BA222" "BA220" "BA210" "BA175" "BA172" "BA158"
## [43] "BA153" "BA145" "BA125" "BA117" "BA113" "BA75"
## [49] "BA69" "BB281" "BB279" "BB259" "BB218" "BB216"
## [55] "BB210" "BB208" "BB198" "BB190" "BB186" "BB182"
## [61] "BB176" "BB167" "BB122" "BB119" "BB102" "CA497"
## [67] "CA415" "CA399" "CA392" "CA384" "CA378" "CA315"
## [73] "CA305" "CA297" "CA289" "CA283" "CA279" "CA261"
## [79] "CA238" "CA233" "CA228" "CA220" "CA217" "CA210"
## [85] "CA198" "CA196" "CA174" "CA167" "CA152C" "CA150"
## [91] "CA140" "CA131" "CA122" "CA96" "CA75" "CB333"
## [97] "CB329" "CB309" "CB280" "CB272" "CB257" "CB246"
## [103] "CB230" "CB216" "CB187" "CB173" "CB172" "CB166"
## [109] "CB162" "CB156" "CB126" "CB115" "CB55" "BD433"
## [115] "BD429" "BD411" "BD371" "BD316C" "BD292" "BD286"
## [121] "BD270" "BD263" "BD251" "BD243" "BD239" "BD209"
## [127] "BD179" "BD175" "BD170" "BD169" "BD143" "BD130"
## [133] "BD115" "BD99" "BD68" "BD55" "BD189C" "AA153C"
## [139] "AA296C" "AA346C" "AA374C" "AA454C" "BA245C" "BA279C"
## [145] "BA396C" "CA183C" "CA258C" "CB263C" "BB103C" "AAT217"
## [151] "AAT261" "AAT240" "AAT278" "AAT39" "AAT211" "AAT222"
## [157] "AAT374" "AAT372" "AAT296" "AAT230" "AAT308" "AG19"
## [163] "AAT364" "AAT300" "CYCB" "AAT242" "BC546" "BC542"
## [169] "BC512" "BC506" "BC498" "BC478" "BC392" "BC379"
## [175] "BC376" "BC374" "BC334" "BC330" "BC321" "BC266"
## [181] "BC243" "BC219" "BC216" "BC199" "BC192" "BC167"
## [187] "BC135" "BC131" "BC126" "BC125" "BC108" "BC83"
## [193] "BC80" "BC70" "BC586C" "BC194C" "BC128C" "CC540"
## [199] "CC531" "CC457" "CC450" "CC447" "CC402" "CC392"
## [205] "CC387" "CC381" "CC378" "CC371" "CC359" "CC330"
## [211] "CC286" "CC283" "CC270" "CC262" "CC150" "CC149"
## [217] "CC138" "CC132" "CC130" "CC126" "CC124" "CC114"
## [223] "CC93" "CC61" "CC385C" "CC338C" "CC171C" "AAT312"
## [229] "AAT283" "LFY" "AAT333" "AP3" "MgSTS17" "MgSTS18"
## [235] "MgSTS21" "MgSTS25" "MgSTS22" "MgSTS27" "MgSTS26" "MgSTS23"
## [241] "MgSTS28" "MgSTS105" "MgSTS120" "MgSTS93" "MgSTS133" "MgSTS58"
## [247] "MgSTS55" "MgSTS40" "MgSTS98" "MgSTS45" "MgSTS11" "MgSTS132"
## [253] "MgSTS212" "MgSTS228" "MgSTS229" "MgSTS234" "MgSTS308" "MgSTS316"
## [259] "MgSTS323" "MgSTS36" "MgSTS43" "MgSTS437" "MgSTS48" "MgSTS49"
## [265] "MgSTS59" "MgSTS68" "MgSTS508" "MgSTS529" "MgSTS455" "MgSTS468"
## [271] "MgSTS480" "MgSTS474" "MgSTS113" "MgSTS106" "MgSTS69" "MgSTS56"
## [277] "MgSTS31" "MgSTS95" "MgSTS262" "MgSTS50" "MgSTS76" "MgSTS388"
## [283] "MgSTS330" "MgSTS332" "MgSTS326" "MgSTS282B" "MgSTS282A" "MgSTS255"
## [289] "MgSTS350" "MgSTS362" "MgSTS344" "MgSTS37" "MgSTS34" "MgSTS426"
## [295] "MgSTS453" "MgSTS456" "MgSTS457" "MgSTS492" "MgSTS513" "MgSTS509"
## [301] "MgSTS500" "MgSTS430" "MgSTS381" "MgSTS314" "MgSTS251" "MgSTS351"
## [307] "MgSTS347" "MgSTS320" "MgSTS293" "MgSTS578" "MgSTS571" "MgSTS574B"
## [313] "MgSTS574a" "MgSTS579" "MgSTS638" "MgSTS590" "MgSTS589" "MgSTS586"
## [319] "MgSTS535" "MgSTS537" "MgSTS538" "MgSTS536" "MgSTS539" "MgSTS563"
## [325] "MgSTS558" "MgSTS419" "MgSTS611" "MgSTS632" "MgSTS609" "MgSTS600"
## [331] "MgSTS565" "MgSTS606" "MgSTS577" "MgSTS438" "MgSTS477" "MgSTS383"
## [337] "MgSTS504A" "MgSTS504B" "MgSTS504C" "MgSTS545" "MgSTS542A" "MgSTS542B"
## [343] "MgSTS598" "MgSTS441" "MgSTS104" "MgSTS511" "MgSTS621" "MgSTS622"
## [349] "MgSTS459" "MgSTS220" "MgSTS214" "MgSTS467" "MgSTS470" "MgSTS599"
## [355] "MgSTS431" "MgSTS440"
no_dist = select_segreg(data_seg, distorted = FALSE, numbers = TRUE)
no_dist
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19
## [19] 20 21 22 23 24 25 26 27 28 29 30 32 33 34 35 36 37 38
## [37] 39 40 42 44 45 46 47 48 50 51 52 53 54 56 57 58 59 60
## [55] 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
## [73] 79 80 81 82 83 86 87 88 89 91 92 93 94 95 96 97 98 99
## [91] 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
## [109] 118 119 120 121 122 123 124 125 126 128 129 130 131 132 133 134 136 137
## [127] 138 139 141 142 143 144 145 147 148 149 150 152 153 154 155 156 157 158
## [145] 159 160 161 163 164 165 167 169 170 171 172 173 174 178 179 180 182 183
## [163] 184 185 186 187 188 189 190 191 192 193 194 196 197 198 199 200 201 202
## [181] 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 219 220 221
## [199] 222 223 224 225 226 227 228 229 230 231 232 234 236 237 238 239 240 241
## [217] 242 243 244 245 246 247 248 249 251 252 253 254 255 256 257 258 259 261
## [235] 263 266 267 268 269 270 271 272 273 277 278 279 280 281 282 283 284 287
## [253] 288 289 290 291 293 294 295 296 297 298 299 300 301 302 304 307 308 309
## [271] 310 311 312 313 314 315 316 317 319 320 322 324 325 327 328 329 330 331
## [289] 332 334 336 338 339 340 341 342 343 345 346 347 348 349 350 352 354 355
## [307] 356 357 358 360 361 362 363 364 365 366 367 369 370 371 372 373 374 376
## [325] 379 381 382 383 384 385 386 387 388 390 393 395 396 397 398 399 400 401
## [343] 402 403 405 406 407 408 409 410 411 412 413 414 415 416
plot(data_seg)
LOD_sug = suggest_lod(data_bins)
LOD_sug
## [1] 5.425686
twopts = rf_2pts(input.obj = data_bins, LOD = LOD_sug, max.rf = 0.5)
## Computing 86320 recombination fractions:
##
## 0% .................................................. 82%
## 82% ................................. 100%
mark_no_dist = make_seq(twopts, c(no_dist))
lgs = group(mark_no_dist)
## Selecting markers:
## group 1
## ......
## group 2
## .....................
## group 3
## ............................................................
## ......................
## group 4
## ......................................
## group 5
## ..............
## group 6
## ..................................................
## group 7
## ...............................
## group 8
## .........................
## group 9
## ............
## group 10
## .....
## group 11
## .......................
## group 12
## ....................
## group 13
## .....
## group 14
## ..
set_map_fun(type = "kosambi")
LGs_hmm_safe = LGs_hmm_all = vector("list", length = c(lgs$n.groups))
for (i in 1:lgs$n.groups) {
LGs = make_seq(lgs, i)
LG_hmm = order_seq(LGs, n.init = 5, subset.search = "twopt", twopt.alg = "rcd", THRES = 3)
LG_safe = make_seq(LG_hmm, "safe")
LG_all = make_seq(LG_hmm, "force")
LGs_hmm_safe[[i]] = LG_safe
LGs_hmm_all[[i]] = LG_all
}
g1 = rf_graph_table(LGs_hmm_all[[1]], mrk.axis = "none")
g2 = rf_graph_table(LGs_hmm_all[[2]], mrk.axis = "none")
grid.arrange(g1, g2, ncol=2)
g3 = rf_graph_table(LGs_hmm_all[[3]], mrk.axis = "none")
g4 = rf_graph_table(LGs_hmm_all[[4]], mrk.axis = "none")
grid.arrange(g3, g4, ncol=2)
g5 = rf_graph_table(LGs_hmm_all[[5]], mrk.axis = "none")
g6 = rf_graph_table(LGs_hmm_all[[6]], mrk.axis = "none")
grid.arrange(g5, g6, ncol=2)
g7 = rf_graph_table(LGs_hmm_all[[7]], mrk.axis = "none")
g8 = rf_graph_table(LGs_hmm_all[[8]], mrk.axis = "none")
grid.arrange(g7, g8, ncol=2)
g9 = rf_graph_table(LGs_hmm_all[[9]], mrk.axis = "none")
g10 = rf_graph_table(LGs_hmm_all[[10]], mrk.axis = "none")
grid.arrange(g9, g10, ncol=2)
g11 = rf_graph_table(LGs_hmm_all[[11]], mrk.axis = "none")
g12 = rf_graph_table(LGs_hmm_all[[12]], mrk.axis = "none")
grid.arrange(g11, g12, ncol=2)
g13 = rf_graph_table(LGs_hmm_all[[13]], mrk.axis = "none")
g14 = rf_graph_table(LGs_hmm_all[[14]], mrk.axis = "none")
grid.arrange(g13, g14, ncol=2)
map_1 = list ()
map_1[[1]] = c("CC138","BA153","AA173C","BA214","AAT267","BA129",
"CA389C","CA174","BA416","BA374","AAT225","AAT333")
map_1[[2]] = c("CC385C","BA125","AA420","CC130","CA228","BC167",
"BA172","CB280","BA175","CC132","BD99","CA279")
map_1[[3]] = c("CC378","BD286","CA220","CA238","CB156","BA75",
"BA384","CA131","AA404","BD429","BC586C","BC70")
map_1[[4]] = c("CB329","CA399","CA415","CA233","AA374C","CA497",
"CA183C","AA166C","CA384","BD239","BA279C","BA113",
"BC321","CC270","CB257","AAT367","AA384")
map_1[[5]] = c( "BB186","CC124","BA69","BB210","BD316C","AA378",
"AA268","CC342","AA454C","AA163","BC506","AA118C")
map_1[[6]] = c("AAT230","BD179","AA277","AA158","BD169","CC171C",
"AAT300","CC381","CA283","CC126","BC392","AA371C")
map_1[[7]] = c("BD209","CA258C","AA280","CB173","BB103C","AA361",
"BD170","AAT261","BB102")
map_1[[8]] = c("BA372","CA210","CYCB","CA305","CC450","AAT39",
"AAT211","CB272","BA314","CA122","CC338C","AAT217",
"CC359","BB167","BA158")
map_1[[9]] = c("CA217","CA167","BB218","BC108","BA396C","LFY",
"BA311","AA95","CA196","CA261","CB115","AAT222",
"BC83")
map_1[[10]] = c("CB309","AAT283","BD433","AA153C","AA100","BB259",
"BB122","AAT374","CA289","BB281","CA96","BA497",
"CC392","AAT372","BB190")
map_1[[11]] = c("CC61","BC526C","BA387","CC53","BD340","AAT356",
"BD100","BA196","BB124","CYCA","BC374")
map_1[[12]] = c("BA394","CC114","BD143","BA245C","BA175","AAT308",
"AAT364","BC330","AA296C","CA378","CB216","CA140",
"BB182")
map_1[[13]] = c( "BB198","BC199","BA145","AAT240","CB126","CB263C",
"CB55","BA334","CB172")
map_1[[14]] = c("BC542","CA267","BB216","BD251","CA75","BD371",
"CC93","AA137","BC80","CC320")
map_2 = list ()
map_2[[1]] = data_seg$Marker[LGs_hmm_all[[1]]$seq.num]
map_2[[2]] = data_seg$Marker[LGs_hmm_all[[2]]$seq.num]
map_2[[3]] = data_seg$Marker[LGs_hmm_all[[3]]$seq.num]
map_2[[4]] = data_seg$Marker[LGs_hmm_all[[4]]$seq.num]
map_2[[5]] = data_seg$Marker[LGs_hmm_all[[5]]$seq.num]
map_2[[6]] = data_seg$Marker[LGs_hmm_all[[6]]$seq.num]
map_2[[7]] = data_seg$Marker[LGs_hmm_all[[7]]$seq.num]
map_2[[8]] = data_seg$Marker[LGs_hmm_all[[8]]$seq.num]
map_2[[9]] = data_seg$Marker[LGs_hmm_all[[9]]$seq.num]
map_2[[10]] = data_seg$Marker[LGs_hmm_all[[10]]$seq.num]
map_2[[11]] = data_seg$Marker[LGs_hmm_all[[11]]$seq.num]
map_2[[12]] = data_seg$Marker[LGs_hmm_all[[12]]$seq.num]
map_2[[13]] = data_seg$Marker[LGs_hmm_all[[13]]$seq.num]
map_2[[14]] = data_seg$Marker[LGs_hmm_all[[14]]$seq.num]
compare = matrix(nrow = 14, ncol =14)
for (i in 1:14) {
map_2[[i]]
for (j in 1:14)
compare[i,j] = sum(map_2[[i]] %in% map_1[[j]])
}
compare
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
## [1,] 4 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 11 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 12 0 0 0 9 0 0 15 0 0 0
## [4,] 0 0 0 16 0 0 0 0 0 0 0 0 0
## [5,] 0 0 0 0 10 0 0 0 0 0 0 0 0
## [6,] 0 0 0 0 0 12 0 0 0 0 0 0 0
## [7,] 0 0 0 0 0 0 0 15 0 0 0 0 0
## [8,] 0 0 0 0 0 0 0 0 13 0 0 0 0
## [9,] 0 0 0 0 0 0 0 0 0 0 0 0 0
## [10,] 0 0 0 0 0 0 0 0 0 0 1 0 0
## [11,] 0 1 0 0 0 0 0 0 0 0 0 13 0
## [12,] 0 0 0 0 0 0 0 0 0 0 0 0 9
## [13,] 2 0 0 0 0 0 0 0 0 0 0 0 0
## [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0
## [,14]
## [1,] 0
## [2,] 0
## [3,] 0
## [4,] 0
## [5,] 0
## [6,] 0
## [7,] 0
## [8,] 0
## [9,] 6
## [10,] 0
## [11,] 0
## [12,] 0
## [13,] 0
## [14,] 1
rf_graph_table(LGs_hmm_all[[3]], mrk.axis = "numbers")
LG3 = LGs_hmm_all[[3]]
LG3 = drop_marker(LG3, c(234,220,130, 236,403))
LG3 = map(LG3)
LG3 = group(LG3, LOD = LOD_sug)
## Selecting markers:
## group 1
## ...................................
## group 2
## ......................
## group 3
## ..................
LG3_hmm_safe = LG3_hmm_all = vector("list", length = c(LG3$n.groups))
for (i in 1:LG3$n.groups) {
LGs = make_seq(LG3, i)
LG3_hmm = order_seq(input.seq = LGs, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)
LG3_safe = make_seq(LG3_hmm, "safe")
LG3_all = make_seq(LG3_hmm, "force")
LG3_hmm_safe[[i]] = LG3_safe
LG3_hmm_all[[i]] = LG3_all
}
g1 = rf_graph_table(LG3_hmm_all[[1]], mrk.axis = "none")
g2 = rf_graph_table(LG3_hmm_all[[2]], mrk.axis = "none")
g3 = rf_graph_table(LG3_hmm_all[[3]], mrk.axis = "none")
grid.arrange(g1, g2, g3, ncol=3)
# Linkage groups of the new map (16 groups)
map_3 = list ()
map_3[[1]] = data_seg$Marker[LGs_hmm_all[[1]]$seq.num]
map_3[[2]] = data_seg$Marker[LGs_hmm_all[[2]]$seq.num]
map_3[[3]] = data_seg$Marker[LG3_hmm_all[[1]]$seq.num]
map_3[[4]] = data_seg$Marker[LG3_hmm_all[[2]]$seq.num]
map_3[[5]] = data_seg$Marker[LG3_hmm_all[[3]]$seq.num]
map_3[[6]] = data_seg$Marker[LGs_hmm_all[[4]]$seq.num]
map_3[[7]] = data_seg$Marker[LGs_hmm_all[[5]]$seq.num]
map_3[[8]] = data_seg$Marker[LGs_hmm_all[[6]]$seq.num]
map_3[[9]] = data_seg$Marker[LGs_hmm_all[[7]]$seq.num]
map_3[[10]] = data_seg$Marker[LGs_hmm_all[[8]]$seq.num]
map_3[[11]] = data_seg$Marker[LGs_hmm_all[[9]]$seq.num]
map_3[[12]] = data_seg$Marker[LGs_hmm_all[[10]]$seq.num]
map_3[[13]] = data_seg$Marker[LGs_hmm_all[[11]]$seq.num]
map_3[[14]] = data_seg$Marker[LGs_hmm_all[[12]]$seq.num]
map_3[[15]] = data_seg$Marker[LGs_hmm_all[[13]]$seq.num]
map_3[[16]] = data_seg$Marker[LGs_hmm_all[[14]]$seq.num]
compare = matrix(nrow = 16, ncol =14)
for (i in 1:16) {
map_3[[i]]
for (j in 1:14)
compare[i,j] = sum(map_3[[i]] %in% map_1[[j]])
}
compare
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
## [1,] 4 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 11 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 15 0 0 0
## [4,] 0 0 11 0 0 0 0 0 0 0 0 0 0
## [5,] 0 0 0 0 0 0 9 0 0 0 0 0 0
## [6,] 0 0 0 16 0 0 0 0 0 0 0 0 0
## [7,] 0 0 0 0 10 0 0 0 0 0 0 0 0
## [8,] 0 0 0 0 0 12 0 0 0 0 0 0 0
## [9,] 0 0 0 0 0 0 0 15 0 0 0 0 0
## [10,] 0 0 0 0 0 0 0 0 13 0 0 0 0
## [11,] 0 0 0 0 0 0 0 0 0 0 0 0 0
## [12,] 0 0 0 0 0 0 0 0 0 0 1 0 0
## [13,] 0 1 0 0 0 0 0 0 0 0 0 13 0
## [14,] 0 0 0 0 0 0 0 0 0 0 0 0 9
## [15,] 2 0 0 0 0 0 0 0 0 0 0 0 0
## [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0
## [,14]
## [1,] 0
## [2,] 0
## [3,] 0
## [4,] 0
## [5,] 0
## [6,] 0
## [7,] 0
## [8,] 0
## [9,] 0
## [10,] 0
## [11,] 6
## [12,] 0
## [13,] 0
## [14,] 0
## [15,] 0
## [16,] 1
LG1 = LGs_hmm_all[[1]]$seq.num
LG13 = LGs_hmm_all[[13]]$seq.num
seq1.13 = c(LG1, LG13)
seq1.13 = make_seq(twopts, seq1.13)
group_LG1.13 = group(seq1.13, LOD = 4)
## Selecting markers:
## group 1
## ............
LG1.13_order = order_seq(seq1.13)
LG1.13_order = make_seq(LG1.13_order, "force")
rf_graph_table(LG1.13_order, mrk.axis = "numbers")
LG9 = LGs_hmm_all[[9]]$seq.num
LG14 = LGs_hmm_all[[14]]$seq.num
seq9.14 = c(LG9, LG14)
seq9.14 = make_seq(twopts, seq9.14)
group_LG9.14 = group(seq9.14, LOD = 4)
## Selecting markers:
## group 1
## ...............
LG9.14_order = order_seq(seq9.14)
LG9.14_order = make_seq(LG9.14_order, "force")
rf_graph_table(LG9.14_order, mrk.axis = "numbers")
rf_graph_table(LGs_hmm_all[[11]], mrk.axis = "numbers")
compare = map_2[[11]] %in% map_1[[2]]
position = which(compare == TRUE)
position
## [1] 14
LG1 = LG1.13_order
LG2 = LGs_hmm_all[[2]]
LG3 = LG3_hmm_all[[2]]
LG4 = LGs_hmm_all[[4]]
LG5 = LGs_hmm_all[[5]]
LG6 = LGs_hmm_all[[6]]
LG7 = LG3_hmm_all[[3]]
LG8 = LGs_hmm_all[[7]]
LG9 = LGs_hmm_all[[8]]
LG10 = LG3_hmm_all[[1]]
LG11 = LGs_hmm_all[[10]]
LG12 = LGs_hmm_all[[11]]
LG13 = LGs_hmm_all[[12]]
LG14 = LG9.14_order
rf_graph_table(LG1, mrk.axis = "numbers")
LG1_drop1 = drop_marker(LG1, c(257, 1))
LG1_map1 = map(LG1_drop1)
ripple_seq(LG1_map1, ws = 5)
LG1_drop2 = drop_marker(LG1_map1, c(225,28,96))
LG1_map2 = map(LG1_drop2)
LG1_extend_225 = try_seq(LG1_map2, 225)
LG1_extend_225 = make_seq(LG1_extend_225, 3, 1)
rf_graph_table(LG1_extend_225, mrk.axis = "numbers")
LG1_extend_28 = try_seq(LG1_extend_225, 28)
LG1_extend_28 = make_seq(LG1_extend_28, 4, 1)
rf_graph_table(LG1_extend_28, mrk.axis = "numbers")
LG1_extend_96 = try_seq(LG1_extend_28, 96)
LG1_extend_96 = make_seq(LG1_extend_96, 5, 1)
LG1_final = LG1_extend_96
rf_graph_table(LG1_final, mrk.axis = "numbers")
rf_graph_table(LG2, mrk.axis = "numbers")
LG2_drop1 = drop_marker(LG2, c(251,83))
LG2_map1 = map(LG2_drop1)
ripple_seq(LG2_map1, ws = 5)
LG2_final = LG2_map1
rf_graph_table(LG2_final, mrk.axis = "numbers")
rf_graph_table(LG3, mrk.axis = "numbers")
LG3_drop1 = drop_marker(LG3, c(114,228,117,32,183))
LG3_map1 = map(LG3_drop1)
ripple_seq(LG3_map1, ws = 5)
LG3_final = LG3_map1
rf_graph_table(LG3_final, mrk.axis = "numbers")
rf_graph_table(LG4, mrk.axis = "numbers")
LG4_drop1 = drop_marker(LG4, c(4))
LG4_map1 = map(LG4_drop1)
ripple_seq(LG4_map1, ws = 5)
LG4_drop2 = drop_marker(LG4_map1, c(238,110,291,125,76))
LG4_map2 = map(LG4_drop2)
LG4_extend_238 = try_seq(LG4_map2, 238)
LG4_extend_238 = make_seq(LG4_extend_238, 1, 1)
rf_graph_table(LG4_extend_238, mrk.axis = "numbers")
LG4_extend_110 = try_seq(LG4_extend_238, 110)
LG4_extend_110 = make_seq(LG4_extend_110, 2, 1)
rf_graph_table(LG4_extend_110, mrk.axis = "numbers")
LG4_extend_291 = try_seq(LG4_extend_110, 291)
LG4_extend_291 = make_seq(LG4_extend_291, 3, 1)
rf_graph_table(LG4_extend_291, mrk.axis = "numbers")
LG4_final = drop_marker(LG4_extend_291, c(145,158))
LG4_final = map(LG4_final)
rf_graph_table(LG4_final, mrk.axis = "numbers")
rf_graph_table(LG5, mrk.axis = "numbers")
LG5_drop1 = drop_marker(LG5, c(191))
LG5_map1 = map(LG5_drop1)
ripple_seq(LG5_map1, ws = 5)
LG5_final = LG5_map1
rf_graph_table(LG5_final, mrk.axis = "numbers")
rf_graph_table(LG6, mrk.axis = "numbers")
LG6_drop1 = drop_marker(LG6, c(6,203,310,212,149))
LG6_map1 = map(LG6_drop1)
ripple_seq(LG6_map1, ws = 5)
LG6_final = LG6_map1
rf_graph_table(LG6_final, mrk.axis = "numbers")
rf_graph_table(LG7, mrk.axis = "numbers")
LG7_drop1 = drop_marker(LG7, c(148,118,71,115))
LG7_map1 = map(LG7_drop1)
rf_graph_table(LG7_map1, mrk.axis = "numbers")
ripple_seq(LG7_map1, ws = 5)
LG7_final = LG7_map1
rf_graph_table(LG7_final, mrk.axis = "numbers")
rf_graph_table(LG8, mrk.axis = "numbers")
LG8_drop1 = drop_marker(LG8, c(46))
LG8_map1 = map(LG8_drop1)
ripple_seq(LG8_map1, ws = 5)
LG8_final = LG8_map1
rf_graph_table(LG8_final, mrk.axis = "numbers")
rf_graph_table(LG9, mrk.axis = "numbers")
LG9_drop1 = drop_marker(LG9, c(27,226,17))
LG9_map1 = map(LG9_drop1)
ripple_seq(LG9_drop1, ws = 5)
LG9_extend_117 = try_seq(LG9_map1, 17)
LG9_extend_117 = make_seq(LG9_extend_117, 12, 1)
LG9_final = LG9_extend_117
rf_graph_table(LG9_final, mrk.axis = "numbers")
rf_graph_table(LG10, mrk.axis = "numbers")
LG10_drop1 = drop_marker(LG10, c(255,107,406,327,123))
LG10_map1 = map(LG10_drop1)
ripple_seq(LG10_map1, ws = 5)
LG10_final = LG10_map1
rf_graph_table(LG10_map1, mrk.axis = "numbers")
rf_graph_table(LG11, mrk.axis = "numbers")
ripple_seq(LG11, ws = 5)
rf_graph_table(LG12, mrk.axis = "numbers")
LG12_drop1 = drop_marker(LG12, c(30,44, 193,204,241))
LG12_map1 = map(LG12_drop1)
ripple_seq(LG12_map1, ws = 5)
LG12_final = LG12_map1
rf_graph_table(LG12_final, mrk.axis = "numbers")
rf_graph_table(LG13, mrk.axis = "numbers")
LG13_drop1 = drop_marker(LG13, c(116))
LG13_map1 = map(LG13_drop1)
ripple_seq(LG13_map1, ws = 5)
LG13_final = LG13_map1
rf_graph_table(LG13_final, mrk.axis = "numbers")
rf_graph_table(LG14, mrk.axis = "numbers")
ripple_seq(LG14, ws = 5)
LG14_drop1 = drop_marker(LG14, c(215,99,258,21))
LG14_map1 = map(LG14_drop1)
LG14_extend_21 = try_seq(LG14_map1, 21)
LG14_extend_21 = make_seq(LG14_extend_21, 2, 1)
rf_graph_table(LG14_extend_21, mrk.axis = "numbers")
LG14_extend_215 = try_seq(LG14_extend_21, 215)
LG14_extend_215 = make_seq(LG14_extend_215, 1, 1)
rf_graph_table(LG14_extend_215, mrk.axis = "numbers")
LG14_extend_99 = try_seq(LG14_extend_215, 99)
LG14_extend_99 = make_seq(LG14_extend_99, 1, 1)
rf_graph_table(LG14_extend_99, mrk.axis = "numbers")
LG14_extend_258 = try_seq(LG14_extend_99, 258)
LG14_extend_258 = make_seq(LG14_extend_258, 1, 1)
LG14_final = LG14_extend_258
rf_graph_table(LG14_final, mrk.axis = "numbers")
map_4 = list ()
map_4[[1]] = data_seg$Marker[LG1_final$seq.num]
map_4[[2]] = data_seg$Marker[LG2_final$seq.num]
map_4[[3]] = data_seg$Marker[LG3_final$seq.num]
map_4[[4]] = data_seg$Marker[LG4_final$seq.num]
map_4[[5]] = data_seg$Marker[LG5_final$seq.num]
map_4[[6]] = data_seg$Marker[LG6_final$seq.num]
map_4[[7]] = data_seg$Marker[LG7_final$seq.num]
map_4[[8]] = data_seg$Marker[LG8_final$seq.num]
map_4[[9]] = data_seg$Marker[LG9_final$seq.num]
map_4[[10]] = data_seg$Marker[LG10_final$seq.num]
map_4[[11]] = data_seg$Marker[LG11$seq.num]
map_4[[12]] = data_seg$Marker[LG12_final$seq.num]
map_4[[13]] = data_seg$Marker[LG13_final$seq.num]
map_4[[14]] = data_seg$Marker[LG14_final$seq.num]
compare = matrix(nrow = 14, ncol =14)
for (i in 1:14) {
map_4[[i]]
for (j in 1:14)
compare[i,j] = sum(map_4[[i]] %in% map_1[[j]])
}
compare
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
## [1,] 5 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 9 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 10 0 0 0 0 0 0 0 0 0 0
## [4,] 0 0 0 13 0 0 0 0 0 0 0 0 0
## [5,] 0 0 0 0 9 0 0 0 0 0 0 0 0
## [6,] 0 0 0 0 0 11 0 0 0 0 0 0 0
## [7,] 0 0 0 0 0 0 7 0 0 0 0 0 0
## [8,] 0 0 0 0 0 0 0 14 0 0 0 0 0
## [9,] 0 0 0 0 0 0 0 0 13 0 0 0 0
## [10,] 0 0 0 0 0 0 0 0 0 12 0 0 0
## [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0
## [12,] 0 0 0 0 0 0 0 0 0 0 0 11 0
## [13,] 0 0 0 0 0 0 0 0 0 0 0 0 8
## [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0
## [,14]
## [1,] 0
## [2,] 0
## [3,] 0
## [4,] 0
## [5,] 0
## [6,] 0
## [7,] 0
## [8,] 0
## [9,] 0
## [10,] 0
## [11,] 0
## [12,] 0
## [13,] 0
## [14,] 7
draw_map2(LG1_final, LG2_final, LG3_final, LG4_final, LG5_final,
LG6_final, LG7_final, LG8_final, LG9_final, LG10_final, LG11,
LG12_final, LG13_final, LG14_final, tag = "all",
group.names = c("LG1","LG2","LG3", "LG4", "LG5", "LG6", "LG7",
"LG8","LG9","LG10","LG11", "LG12","LG13", "LG14"),
output = "map_final.pdf")
Van Os, H., P. Stam, R. G. Visser, and H. J. Van Eck. Record: a novel method for ordering loci on a genetic linkage map. Theoretical and Applied Genetics 112: 30–40, 2005.